org.jmol.smiles
Class PatternMatcher

java.lang.Object
  org.jmol.smiles.PatternMatcher

All Implemented Interfaces:

SmilesMatcherInterface

public class PatternMatcher
extends java.lang.Object
implements SmilesMatcherInterface

A class to match a SMILES pattern with a Jmol molecule.

The SMILES specification can been found at the SMILES Home Page.

An example on how to use it:

 PatternMatcher matcher = new PatternMatcher(jmolViewer);
 try {
   BitSet bitSet = matcher.getSubstructureSet(smilesString);
   // Use bitSet...
 } catch (InvalidSmilesException e) {
   // Exception management
 }
 

Author:

Nicolas Vervelle

See Also:

SmilesMolecule

Field Summary

private int	atomCount
private ModelSet	modelSet

Constructor Summary

PatternMatcher()
Constructs a PatternMatcher.

Method Summary

java.util.BitSet	getSubstructureSet(SmilesMolecule pattern) Returns a vector of bits indicating which atoms match the pattern.
java.util.BitSet	getSubstructureSet(java.lang.String smiles) Returns a vector of bits indicating which atoms match the pattern.
private void	searchMatch(java.util.BitSet bs, SmilesMolecule pattern, int atomNum) Recursively search matches.
private void	searchMatch(java.util.BitSet bs, SmilesMolecule pattern, SmilesAtom patternAtom, int atomNum, int i) Recursively search matches.
void	setViewer(Viewer viewer)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

atomCount

private int atomCount

modelSet

private ModelSet modelSet

Constructor Detail

PatternMatcher

public PatternMatcher()

Constructs a PatternMatcher.

Method Detail

setViewer

public void setViewer(Viewer viewer)

Specified by:

setViewer in interface SmilesMatcherInterface

getSubstructureSet

public java.util.BitSet getSubstructureSet(java.lang.String smiles)
                                    throws java.lang.Exception

Returns a vector of bits indicating which atoms match the pattern.

Specified by:

getSubstructureSet in interface SmilesMatcherInterface

Parameters:

smiles - SMILES pattern.

Returns:

BitSet Array indicating which atoms match the pattern.

Throws:

java.lang.Exception - Raised if smiles is not a valid SMILES pattern.

getSubstructureSet

public java.util.BitSet getSubstructureSet(SmilesMolecule pattern)

Returns a vector of bits indicating which atoms match the pattern.

Parameters:

pattern - SMILES pattern.

Returns:

BitSet Array indicating which atoms match the pattern.

searchMatch

private void searchMatch(java.util.BitSet bs,
                         SmilesMolecule pattern,
                         int atomNum)

Recursively search matches.

Parameters:

bs - Resulting BitSet (each atom in a structure is set to 1).

pattern - SMILES pattern.

atomNum - Current atom of the pattern.

searchMatch

private void searchMatch(java.util.BitSet bs,
                         SmilesMolecule pattern,
                         SmilesAtom patternAtom,
                         int atomNum,
                         int i)

Recursively search matches.

Parameters:

bs - Resulting BitSet (each atom in a structure is set to 1).

pattern - SMILES pattern.

patternAtom - Atom of the pattern that is currently tested.

atomNum - Current atom of the pattern.

i - Atom number of the atom that is currently tested to match patternAtom.